Entering edit mode
19 months ago
Chris
•
0
I have variants in the format Affx-15447216, Affx-7955848, etc. with no other information to help map them to standard notation. I assume that these are identifiers for the SNP array provided by Affymetrix (I have no details on which platform exactly) but all of the support links appear to be dead (e.g. https://www.affymetrix.com/support/mas/index.affx#1_1). Has anyone run across this before and found a method to convert these variants to a more recognizable standard format?
You can probably find affy annotation at Thermo Fisher. See this related question. And if you google around, even with just those ids listed above, or related information you find, you can find various data files that might have mappings. And FWIW, you can probably resolve them via the table browser at UCSC.
Thanks, I also believe that the mapping exists somewhere on the Thermo Fisher website but I wasn't able to find it following the discussion in that related question. The table browser also has variants in a different format for the SNP arrays (
SNP_A-{int}) with no direct mapping (my identifiers do not match to anySNP_A-{int}identifier in the genome browser by just swapping the prefix).I did follow your advice though and found a mapping table that looks to be a QC list from the UKB. I know these variants are from the UKB so that gives me some confidence that the mappings are valid, and it looks like the best lead so far. The table is here: https://biobank.ctsu.ox.ac.uk/crystal/crystal/auxdata/ukb_snp_qc.txt but I don't know where its referenced from the website. Appreciate the help.
Also, I've found them in the actual
bimfiles for the UKB array data, so I think that would be the official mapping and the most useful if anyone finds this question in the future.Available from here with checksums: https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=1963